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14 months ago
Vikram
•
0
How long does it take for HISAT2 aligner to complete the aligning process ? im using 24 threads and 251RAM. the size of forward and reverse read files is 990MB and 1,4GB respectively. its been more than two hours, and its mentioned in the paper (https://www.nature.com/articles/nprot.2016.095) that it will take less than 20min for the aligning process to complete. if you have used HISAT2, how long did it take and is this normal to take more than two hours and should i kill the process ?
Can you post your command? Are you certain you are actually using 24 threads (i.e your command has
-p 24option in it)?If the size of the output file is increasing then HISAT2 is working. It may not be using 24 threads.
For this, use
topto monitor your job andls -lhto check file sizes over time.